Western University Scholarship@Western Biochemistry Publications Biochemistry Department 6-3-2009 Structural Basis of Error-prone Replication and Stalling at a Thymine Base by Human DNA Polymerase iota Kevin N. Kirouac University of Western Ontario, [email protected] Hong Ling University of Western Ontario, [email protected] Follow this and additional works at: https://ir.lib.uwo.ca/biochempub Part of the Biochemistry Commons Citation of this paper: Kirouac, Kevin N. and Ling, Hong, "Structural Basis of Error-prone Replication and Stalling at a Thymine Base by Human DNA Polymerase iota" (2009). Biochemistry Publications. 66. https://ir.lib.uwo.ca/biochempub/66 Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase ι Kevin N Kirouac & Hong Ling* Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1 *Correspondence should be addressed to H. L . ( [email protected] ) Subject Category: Structural Biology; Genome Stability and Dynamics Characters (with spaces) 48 073 Figures 5 Table 1 Running Title: Polymerase ι misinserts and stalls at T bases Competing interest statement: The authors declare no competing financial interests 1 ABSTRACT Human DNA polymerase ι (pol ιιι) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T), and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol ι complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine:pyrimidine mismatch and excludes Watson-Crick base pairing in pol ιιι. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking while incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H- bonding with Gln59 from the finger domain explains the preferential T:G mismatch. A template ‘U-turn’ is stabilized by pol ι and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain swapping experiments indicate that the finger domain is responsible for pol ιιι’s high error rates on pyrimidines and determines the incorporation specificity. Key Words : Y family DNA polymerase/ pol ι/ incorporation specificity/ mutagenesis/ translesion synthesis 2 INTRODUCTION A strict adherence to Watson-Crick base pairing is a key feature in determining the high fidelity of replicative DNA polymerases. An induced fit mechanism is employed when a correct incoming nucleotide is optimally paired with the template base (Doublie et al., 1999). A highly restrictive active site with limited solvent accessibility enables this efficient base pair selection (Doublie et al., 1998). In contrast, Y family DNA polymerases, which specialize in traversing DNA lesions have evolved an open and solvent accessible active site allowing for permissive base pairing (Ling et al., 2001). The Y-family polymerases contain a similar catalytic core, consisting of “palm”, “finger” and “thumb” domains as in high-fidelity DNA polymerases. The smaller finger and thumb domains in Y-family polymerases generate a solvent-accessible and spacious active site. The finger domain contacts the replicating base pair and is therefore the substrate recognition site. In addition, the Y-family polymerases possess a unique C- terminal domain, called the “little finger” or polymerase associated domain (PAD). The little finger (LF) holds the DNA substrate along with the thumb domain. Around the active site, the major groove of the DNA duplex is fully solvent exposed. Thus, bulky DNA adducts can be accommodated in the active site and multiple nucleotide conformations can be adopted in order for the enzyme to replicate through the lesion. The caveat to performing translesion DNA synthesis is a high error rate of replication on undamaged DNA (Boudsocq et al., 2001; Johnson et al., 2000; Zhang et al., 2000). Human Y family DNA polymerase ι (pol ι) is a specialized polymerase that does not utilize Watson-Crick base pairing for DNA replication. Instead, this enzyme functions by inducing a syn conformation on template purines, which results in 3 Hoogsteen base pairing with the correctly matched incoming nucleotide (Johnson et al., 2005; Nair et al., 2005; Nair et al., 2006). The ability to induce a nucleotide syn conformation by pol ι appears to serve as the mechanism for replication opposite damaged template purines. Structural evidence demonstrates that the 1, N6 ethenodeoxyadenosine and N2 ethyl guanine lesions are presented in the syn conformation protruding into the solvent accessible major groove of the DNA helix (Nair et al., 2006; Pence et al., 2008), which allows base pairing with the correct incoming nucleotide. DNA replication by pol ι on template pyrimidines displays extremely high error rates, while incorporation opposite template purines is more accurate (Kunkel et al., 2003; Tissier et al., 2001; Tissier et al., 2000; Zhang et al., 2000). Opposite a template thymine (T), pol ι prefers to incorporate a guanine (G) up to 2.5 fold over the correctly paired adenine (A) in a metal-dependent manner (Frank and Woodgate, 2007). In addition, pol ι has inefficient replication past a template T base causing a signature T template stall (Zhang et al., 2000). A similar pattern of misincorporation and replication stalling by pol ι is observed opposite template uracil (U) (Vaisman and Woodgate, 2001). It has been proposed that G misincorporation opposite template U could restore the genomic sequence of cytosines (C) that have undergone deamination. The biological role of this preferred misinsertion of G opposite template T or U within cells remains unknown. However, such an unusual and highly specific property could serve a unique function in DNA maintenance. The error-prone replication on template T by pol ι has been implicated in the high rates of DNA mutagenesis presented in patients with the UV-sensitive disorder; Xeroderma Pigmentosum Variant (XP-V) syndrome (Wang et al., 2007). When the 4 human Y family DNA polymerase η (pol η) is inactivated by mutations, pol ι takes over its specialized role of bypassing UV-induced thymine-thymine (T-T) dimers. However, the preference of misinsertion opposite template T by pol ι results in an increase in mutagenesis and the presentation of the disease. Although pol ι is responsible for increased DNA mutagenesis when functioning out of context, this enzyme does appear to play a role in tumour suppression. Mice deficient in both pol η and pol ι have an earlier onset on UV-light induced tumors than pol η deficiency alone (Dumstorf et al., 2006; Ohkumo et al., 2006), indicating a role for pol ι in UV-induced lesion bypass. In addition, it has recently been observed that pol ι plays a significant role in cellular protection from oxidative damage (Petta et al., 2008). Although pol ι likely facilitates the repair of oxidative DNA lesions, the specificity and mechanism of this repair is unknown. The unique T template misincorporation by pol ι has been extensively reported, but has remained mechanistically unexplained. Here, we report three crystal structures of pol ι in complex with DNA containing a template T base in the active site, which is paired with either correct (A) or incorrect (T or G) incoming nucleotides. Our results reveal, for the first time, the structural basis of preferred G misincorporation and stalling on a template T base by pol ι. RESULTS Pol ι-DNA-dNTP complexes with template bending back at the T base In order to position the thymine base at the pol ι active site, DNA substrates for crystallization were designed containing a thymine 5´ to the template-primer junction. The first (substrate 1) is a 15/9-nt duplex DNA with two thymines 5 ' to the template- 5 primer junction (see Methods). The second (substrate 2) is an 18-nt self-complementary duplex (14 base pairs) containing a 2, 3-dideoxy 3’ primer end for trapping ternary complexes (see Methods). Incoming 2, 3-dideoxy ATP (ddATP) was incubated with DNA substrate 1 and co-crystallized with pol ι, while dGTP and dTTP were incubated with DNA substrate 2 and co-crystallized with pol ι. Interestingly, the pol ι-DNA-ddATP complex was trapped at the first T from the template-primer junction without the expected one incorporation, probably due to the replication stalling at T. The resulting three crystal structures are denoted as T:ddADP, T:dGTP and T:dTTP according to the replicating base pair in the active site. The ternary complex crystals are in two different space groups (C2 for T:ddADP; P6 522 for T:dGTP and T:dTTP) and diffract to 2.0 Å, 2.0 Å, and 2.2 Å resolutions, respectively (Table I). In T:ddADP, incoming ddATP was hydrolyzed to ddADP. Hydrolysis in this manner has been observed in Dpo4 from Sulfolobus solfataricus , the model enzyme of the Y-family DNA polymerase, due to a weak phosphatase activity of the polymerase (Ling et al., 2001). In the T:ddADP structure, the active site metal ions have been refined as Ca 2+ , due to the presence of 150 mM CaCl 2 in the crystallization buffer and the high electron density. In addition, anomalous signal peaks were observed at the metal ion sites which are distinct from surrounding non-metal atoms though weak at the A site (Figure 4S). This is analogous to Dpo4 structures crystallized with 100 mM Ca(AC) 2 (Ling et al., 2001; Wong et al., 2008). Such anomalous peaks were not observed for the T:dTTP or T:dGTP structures, which were crystallized in the absence of Ca 2+ ions (Figure 5S). Thus, the T:dTTP and T:dGTP structures were refined with two active site Mg 2+ ions.